Interpretive Summary: This book chapter describes the proposed process of evolution of Citrus tristeza virus (CTV) based upon genetic sequence from several isolates of CTV. The chapter describes the likely mechanism(s) of evolution based upon the known genetic sequences and explains why current populations of CTV are very diverse. The chapter also proposes, based upon the mechanisms of evolution described in the chapter, that there are many genetically diverse CTV isolates than have been detected so far. These potential new CTV pose a problem for the regulation and detection of CTV, since it suggests that we know of only a portion of the CTV isolates and that new and better diagnostic tools are needed in the continuing program of control of CTV and the numerous CTV-related diseases.

Technical Abstract:
Citrus tristeza virus (CTV) isolates T36, T68-1 and NS25 showed phylogenetic incongruities between sequences involved in viral RNA replication and those involved in movement and other viral functions. This incongruity was not found in the sequences of isolates T3, T30, T385, VT and T318A. Distance analysis of the replication sequences of T36, T68-1 and NS25 showed these sequences were distinct from each other and from replication sequences of T3, T30, T385, VT and T318A, which formed a cluster of related replication sequences. Distance analysis indicated that sequences not associated with replication were highly similar among all CTV sequences examined. Phylogenetic profiling identified potential recombination points in the genomes of T36, T68-1 and NS25, indicating that recombination joined disparate replication sequences with highly conserved sequences for movement and other virus functions. CTV is restricted primarily to host plants in the genus Citrus and the evidence suggests that the CTV genome has evolved into two functional modules with major increases in genetic diversity in the replication module occurring when more distantly related replication sequences are introduced into infected citrus trees and recombination occurs with these more conserved CTV sequences for movement and other virus functions associated with a CTV population already present in these infected citrus trees.